Short tandem repeat (STR) DNA sequences are interspersed throughout the human genome at up to several hundred thousand loci. These loci are highly polymorphic with respect to the number of repeat units they contain and may vary in internal structure as well. Variation in the number of STR repeat units at a particular locus causes the length of the DNA at that locus to vary from allele to allele.
While the alleles at a single STR locus may be the same for two different individuals in a population, especially if the individuals are genetically related, the probability that the alleles of two individuals will be identical at several different loci becomes smaller and smaller as the number of loci examined increases. By determining the alleles at a sufficiently large number of loci in two different DNA samples it is possible to establish with virtual certainty whether or not the two samples originally came from the same individual.
Characterization of the alleles at specific STR loci for purposes of individual identification usually begins with the PCR amplification of genomic DNA. A primer pair that hybridizes to unique DNA sequences that flank the repeat region are used to amplify the STR locus. By using multiple primer pairs, it is possible to amplify multiple STR loci in the same reaction; a technique referred to as multiplexing. The resulting PCR products can be separated by electrophoresis and identified by comparison to known DNA standards.
Though techniques for analyzing STR loci, especially using capillary electrophoresis (CE) and fluorescent detection have been known and utilized for 20 years or so, there remains a need for new methods and compositions for analyzing STR loci. Disclosed herein are methods, compositions and kits for expanding the functionality of CE generally and for forensic analysis in particular.